Friday, October 21, 2011

Eurogenes is upset

Eurogenes seems to be upset this week, first throwing a tantrum at Dr. McDonald and then at myself. You can probably find the cached text in Google for some time, although Eurogenes has deleted his anti-McDonald tantrum, and changed the verbiage on the one directed against me on advice of some more cool-headed people. Here is the epilogue of his original anti-Dienekes rant:

Dienekes, you've got a spreadsheet online showing all sorts of weird things. You need stop being a prat, and do something about it ASAP.

Eurogenes' animus towards me is not surprising for those who have followed our interactions since the old days. Of course he is benefiting from my work (I have pointed him towards data he didn't know existed, he is using DIYDodecad, as well as the 1000Genomes data extracted with my code by the MDLP), so one would think that if he had any criticism against me, he would at least express it in a more dignified way.

Of course, being rude, ungrateful and mean-spirited does not mean one is wrong! So, what has Eurogenes actually discovered?

He noted the high Ukrainian West/East European ratio produced by Dodecad v3, and objected to my idea that Ukrainians were transitional to the Balkans and the Caucasus. Actually, according to the PCA plot of the Yunusbayev et al. (2011) paper, they are transitional, being situated toward both the Balkans and the Caucasus, relative to Belorussians/Lithuanians, i.e., the populations that generally show peaks of East European-related components. This is also supported by the ADMIXTURE analysis that reveals Ukrainians to possess a Caucasus-centered component largely lacking in other Eastern Slavs, but shared with Balkan/Caucasus populations.

Should I have not tested the new Yunusbayev data with Dodecad v3 and reported their results? Of course not. When one has a measuring instrument, one uses it on new data to test its performance and reports what he sees. This is exactly what I have done. At the same time, one uses the new data to create new measuring instruments that have been trained using all available data, which is also what I have done with euro7 and the upcoming Dodecad v4.

To make matters worse, Eurogenes suggests that my euro7 analysis agrees with his K=10 which was presented two weeks later. So, apparently, I am posting correct information about Ukrainians 2 weeks before he does, and this means that I am turning around to his way of thinking rather than vice versa. Go figure.

Eurogenes continues with his posting of supposed MDS/PCA plots supporting his thesis. Actually, what he has posted are plots based on metric distances in the space of admixture proportions; these are not genetic distances because e.g., a +/- 1% difference in a Sub-Saharan component results in the same Euclidean distance difference as a +/-1% in a European one, although the former affects genetic distance much more strongly than the latter. Metric distances are fine to quickly determine closeness of samples in the space of admixture proportions, but they are certainly no substitute for real genetic distances. I have already linked above with evidence that Ukrainians are transitional to the Balkans and the Caucasus relative to the Yunusbaeyev et al. populations.

I am also, apparently, accused of neglecting to point out the deficiencies of Dodecad v3, and I am invited by Eurogenes to retract it completely! This proposal is equivalent to the idea that we should burn old topographic maps that were based on measurements with sticks, ropes, and trigonometers, because we can now measure distances with laser beams. And, it is funny indeed that I am supposedly neglecting the deficiencies of Dodecad v3 when, 3 weeks before the Eurogenes rant, I post exactly what its limitations are, and how it can be made better.

It is unfortunate that Eurogenes has chosen to go down that path. Envy is not a good guide to behavior, and perhaps, instead of relishing at the prospect of putting others down, he could spend a little more time inventing something of his own.

UPDATE: In a newer post, Eurogenes attempts to justify his mishandling of MDS, by suggesting that he presented results based on raw SNP data. This is of course nonsense, since Eurogenes does not have the raw SNP data of the Dodecad populations. He is comparing apples and oranges by comparing plots made on raw data with those made in the space of admixture proportions. Furthermore, his supposed findings have no bearing on the Yunusbayev et al. ADMIXTURE and PCA results, posted above.

I have been following the interaction between David and Dienekes for a few years, and it seems to me that there is some sort of hostility (I don't know how big) between them. This is especially apparent in David's attitude toward Dienekes.

Dienekes, you need to make some corrections to that post and to the spreadsheet.

Your explanation that Ukrainians are more Western European than Poles because they're transitional to the Caucasus, simply doesn't work, because Poles are transitional to Western Europe.

You know what happened, so you have to fix it. Either take down that spreadsheet, or modify it so that the unsupervised and supervised samples are separated, and also drop a note why you separated them.

I'm definitely upset that you acted like a prat when I alerted you to this problem on your blog. And I'm going to keep blogging about this issue until you acknowledge it.

"Their ratio is exactly what one might expect from their geographical position vis a vis. Russians, Belorussians, and Balts, i.e., populations with a high E/W ratio."

You imagine that I wrote something about Ukrainians being transitional between Poles and the Caucasus/Balkans, but that is, in fact, not something I wrote. Please do not confirm what was said about you by arguing against imaginary arguments.

The fact that Ukrainians are a little closer to the Balkans and Caucasus is hardly reason to speculate that they should have inverted West/East Euro proportions compared to Belorussians, Russians and Lithuanians.

But that's not even the problem. The problem is that Ukrainians are more Western and less Eastern than Poles in your results. But you don't acknowledge this, and keep on prattling about Belorussians etc.

So tell us, why are Ukrainians in that analysis more Western and less Eastern than Poles?

In fact, is it even possible to produce inverted West/East Euro results for these Ukrainians in an unsupervised run?

Why don't you run some of your highly professional MDS/PCA plots with Ukrainians and Poles, vs Balkan and Caucasus samples, and let's see if you don't get the same results as my amateur efforts.

In fact, is it even possible to produce inverted West/East Euro results for these Ukrainians in an unsupervised run?

Lol, you are incorrigible. I have already done an unsupervised with these Ukrainians. It's called 'euro7', and it was posted 2 weeks before your own K=10 and 3 weeks before your tirade.

And there will be a lot of useless data floating around the net.

I could blog about your ridiculous K=14 where I got messages from half Balkan + half Anatolian Turks about how come they were more West European than West Asian. Or your equally ridiculous run, where a component was centered on only 4 Irishmen.

You give me plenty to write about pretty much any time you open your mouth. Unlike you, however, I have more productive things to do with my time than engage in your bullshit vendetta.

I must say I must agree with the diagnoses: an emotionally/mentally stable person does not need to go around insulting everyone that disagrees with him as you do and have done in the last many years for what I have observed, Mr. David Polako.

Of course you do have the right to get angry and so, occasionally, but you are just a bully in fact. And that is a psychological issue you should look for help with. Friendly advise.

That does not mean that I agree with using that PA as argument: you may be psycho-emotionally hurt and still be right for a lot of things: it's a handicap but not an absolute one.

Going to the grain. You say: "The problem is that Ukrainians are more Western and less Eastern than Poles in your results".

How is that a problem? Ukrainians (senso lato) are the older, less indoeuropeanized population of the whole region.

Also IF the NE component is actually more NORTH-east than north-EAST, as may be inferred from the fact that it's low in the Balcans and Caucasus, it is also consistent.

Of course nobody will question that Ukraine is geographically to the East/SE of Poland but that's trivial when we speak genetics.

Ukraine fell under the dominance of the Chernyakhov culture - Actually if it wasn't for the Turkic nomads, likely the Goths would of withstood the Slavic expansion, like Romania/Moldova and we would have a Germanic nation in eastern Europe.

Also, didn't your past run also show Ukrainians to have unusually high "north European" and "Atlantic" scores compared to the surrounding groups?

The Chernyakhov culture was not solely comprised of Goths, but also other east-Germanic groups like Scirians, Bastarnae, & Heruli. Maybe for Iberia the Goths were nothing but bringers of cultural elements, but in parts of eastern Europe they had a lasting genetic impact. That's why we can see haplogroup I1a as high as 10% in some areas around the Black Sea. Also, lets not forget the Kievan Rus.

I am of the somewhat tenuous opinion that the origins of Y-DNA haplogroup I overall are in Ukraine and immediate surroundings. That area is the Eastern European Paleolithic "refuge" and has clear continuity into Neolithic (Dniepr-Don specially), influencing the Baltic a lot before Kurgan arrival (and, I guess, later within Kurgan flows).

Of course some study might one day prove me wrong, showing that the origin of haplogroup I is Scandinavia (or elsewhere). But I'm still waiting for that paper. So far AFAIK the highest diversity of I falls in or near Ukraine, at least in principle ratifying my initial impression on this lineage and the overall origins of Europeans in Paleolithic populations rather than Neolithic ones (that also but less so).

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